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GB2515944A - Peptide arrays - Google Patents

Peptide arrays Download PDF

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Publication number
GB2515944A
GB2515944A GB1418188.7A GB201418188A GB2515944A GB 2515944 A GB2515944 A GB 2515944A GB 201418188 A GB201418188 A GB 201418188A GB 2515944 A GB2515944 A GB 2515944A
Authority
GB
United Kingdom
Prior art keywords
peptide library
nucleic acid
target molecule
immobilised
molecule
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
GB1418188.7A
Other versions
GB201418188D0 (en
Inventor
Christopher Ullman
Neil Cooley
Laura Frigotto
Pascale Mathonet
Nahida Parveen
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Isogenica Ltd
Original Assignee
Isogenica Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Isogenica Ltd filed Critical Isogenica Ltd
Publication of GB201418188D0 publication Critical patent/GB201418188D0/en
Publication of GB2515944A publication Critical patent/GB2515944A/en
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1062—Isolating an individual clone by screening libraries mRNA-Display, e.g. polypeptide and encoding template are connected covalently
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1075—Isolating an individual clone by screening libraries by coupling phenotype to genotype, not provided for in other groups of this subclass
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • C12P19/30—Nucleotides
    • C12P19/34—Polynucleotides, e.g. nucleic acids, oligoribonucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P21/00—Preparation of peptides or proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B20/00—Methods specially adapted for identifying library members
    • C40B20/04—Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B20/00—Methods specially adapted for identifying library members
    • C40B20/08—Direct analysis of the library members per se by physical methods, e.g. spectroscopy
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B30/00—Methods of screening libraries
    • C40B30/04—Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/52—Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2570/00—Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Hematology (AREA)
  • Medicinal Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Urology & Nephrology (AREA)
  • Analytical Chemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

A method is disclosed for identifying a member of a peptide library that interacts with a target molecule in situ, the method including expressing immobilised nucleic acid molecules to produce the peptide library in a way that each member of the peptide library is immobilised on the nucleic acid molecule from which it was expressed; contacting the immobilised peptide library with the target molecule; and detecting an interaction between at least one member of the peptide library and the target molecule. The method further comprises sequencing the plurality of nucleic acid molecules in situ on the solid support, such that the at least one member of the peptide library that interacts with the target molecule can be immediately identified, at least by the sequence of the nucleic acid molecule from which it was expressed, without requiring additional or secondary analysis or characterising procedures in order to identify the useful members of the library. The target molecules may themselves be comprised within a second nucleic acid or peptide library.
GB1418188.7A 2012-03-15 2013-03-15 Peptide arrays Withdrawn GB2515944A (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB1204605.8A GB2500243A (en) 2012-03-15 2012-03-15 Identifying members of immobilised peptide libraries comprising protein-DNA complexes
PCT/GB2013/050676 WO2013136095A1 (en) 2012-03-15 2013-03-15 Peptide arrays

Publications (2)

Publication Number Publication Date
GB201418188D0 GB201418188D0 (en) 2014-11-26
GB2515944A true GB2515944A (en) 2015-01-07

Family

ID=46052003

Family Applications (2)

Application Number Title Priority Date Filing Date
GB1204605.8A Withdrawn GB2500243A (en) 2012-03-15 2012-03-15 Identifying members of immobilised peptide libraries comprising protein-DNA complexes
GB1418188.7A Withdrawn GB2515944A (en) 2012-03-15 2013-03-15 Peptide arrays

Family Applications Before (1)

Application Number Title Priority Date Filing Date
GB1204605.8A Withdrawn GB2500243A (en) 2012-03-15 2012-03-15 Identifying members of immobilised peptide libraries comprising protein-DNA complexes

Country Status (3)

Country Link
US (1) US20150057162A1 (en)
GB (2) GB2500243A (en)
WO (1) WO2013136095A1 (en)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014189768A1 (en) * 2013-05-19 2014-11-27 The Board Of Trustees Of The Leland Devices and methods for display of encoded peptides, polypeptides, and proteins on dna
WO2015155035A1 (en) 2014-04-07 2015-10-15 Charybdis Vaccines Srl Method for identifying and mapping the epitopes targeted by an antibody response
US11634706B2 (en) 2014-09-18 2023-04-25 The Trustees of the California State University Single-molecule phenotype analysis
ES2826880T3 (en) 2015-05-11 2021-05-19 Illumina Inc Platform for the discovery and analysis of therapeutic agents
US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10550429B2 (en) 2016-12-22 2020-02-04 10X Genomics, Inc. Methods and systems for processing polynucleotides
US11174479B2 (en) 2018-08-13 2021-11-16 The Board Of Trustees Of The Leland Stanford Junior University Devices and methods for display of encoded peptides, PolyPeptides, and proteins on DNA
US20220243360A1 (en) * 2019-06-27 2022-08-04 Roche Sequencing Solutions, Inc. Peptide libraries having enhanced subsequence diversity and methods for use thereof
WO2021030268A2 (en) 2019-08-09 2021-02-18 Nutcracker Therapeutics, Inc. Microfluidic apparatus and methods of use thereof

Citations (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998020159A1 (en) * 1996-11-07 1998-05-14 Ramot University Authority For Applied Research & Industrial Development Ltd. Representations of bimolecular interactions
WO1998037186A1 (en) * 1997-02-18 1998-08-27 Actinova Limited In vitro peptide or protein expression library
WO1999051773A1 (en) * 1998-04-03 1999-10-14 Phylos, Inc. Addressable protein arrays
WO2000014545A1 (en) * 1998-09-03 2000-03-16 Trellis Bioinformatics, Inc. Multihued labels
WO2001042454A2 (en) * 1999-12-09 2001-06-14 Select Therapeutics Inc. Methods for detecting compound interactions using phage display
WO2001090414A1 (en) * 2000-05-19 2001-11-29 Williams Richard B In vitro evolution of nucleic acids and encoded polypeptide
WO2003010176A2 (en) * 2001-07-24 2003-02-06 Oxford Glycosciences (Uk) Ltd Protein-nucleic acid complexes
WO2003045975A2 (en) * 2001-11-27 2003-06-05 Compound Therapeutics, Inc. Solid-phase immobilization of proteins and peptides
WO2004022746A1 (en) * 2002-09-06 2004-03-18 Isogenica Limited In vitro peptide expression libraray
WO2006046042A2 (en) * 2004-10-27 2006-05-04 Domantis Limited Method of selecting polypeptides
WO2006058159A2 (en) * 2004-11-23 2006-06-01 The United States Of America As Represented By The Secretary Of Health And Human Services, Nih Methods and compositions for the ex vivo high-throughput detection of protein/protein interactions
EP1712623A2 (en) * 1997-01-21 2006-10-18 The General Hospital Corporation Selection of proteins using RNA-protein fusions
EP1816192A1 (en) * 2004-10-15 2007-08-08 Japan Science and Technology Agency LINKER FOR CONSTRUCTING mRNA-PUROMYCIN-PROTEIN CONJUGATE
WO2011071943A1 (en) * 2009-12-07 2011-06-16 Prognosys Biosciences, Inc. Peptide display arrays
WO2012139110A2 (en) * 2011-04-08 2012-10-11 Prognosys Biosciences, Inc. Peptide constructs and assay systems

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020168640A1 (en) * 2001-02-22 2002-11-14 Min Li Biochips comprising nucleic acid/protein conjugates
AU2002368488A1 (en) * 2002-12-23 2004-07-14 Affitech As Process for producing an in vitro peptide expression library

Patent Citations (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998020159A1 (en) * 1996-11-07 1998-05-14 Ramot University Authority For Applied Research & Industrial Development Ltd. Representations of bimolecular interactions
EP1712623A2 (en) * 1997-01-21 2006-10-18 The General Hospital Corporation Selection of proteins using RNA-protein fusions
WO1998037186A1 (en) * 1997-02-18 1998-08-27 Actinova Limited In vitro peptide or protein expression library
WO1999051773A1 (en) * 1998-04-03 1999-10-14 Phylos, Inc. Addressable protein arrays
WO2000014545A1 (en) * 1998-09-03 2000-03-16 Trellis Bioinformatics, Inc. Multihued labels
WO2001042454A2 (en) * 1999-12-09 2001-06-14 Select Therapeutics Inc. Methods for detecting compound interactions using phage display
WO2001090414A1 (en) * 2000-05-19 2001-11-29 Williams Richard B In vitro evolution of nucleic acids and encoded polypeptide
WO2003010176A2 (en) * 2001-07-24 2003-02-06 Oxford Glycosciences (Uk) Ltd Protein-nucleic acid complexes
WO2003045975A2 (en) * 2001-11-27 2003-06-05 Compound Therapeutics, Inc. Solid-phase immobilization of proteins and peptides
WO2004022746A1 (en) * 2002-09-06 2004-03-18 Isogenica Limited In vitro peptide expression libraray
EP1816192A1 (en) * 2004-10-15 2007-08-08 Japan Science and Technology Agency LINKER FOR CONSTRUCTING mRNA-PUROMYCIN-PROTEIN CONJUGATE
WO2006046042A2 (en) * 2004-10-27 2006-05-04 Domantis Limited Method of selecting polypeptides
WO2006058159A2 (en) * 2004-11-23 2006-06-01 The United States Of America As Represented By The Secretary Of Health And Human Services, Nih Methods and compositions for the ex vivo high-throughput detection of protein/protein interactions
WO2011071943A1 (en) * 2009-12-07 2011-06-16 Prognosys Biosciences, Inc. Peptide display arrays
WO2012139110A2 (en) * 2011-04-08 2012-10-11 Prognosys Biosciences, Inc. Peptide constructs and assay systems

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
NIEMEYER C M: "The developments of semisynthetic DNA-protein conjugates", TRENDS IN BIOTECHNOLOGY, ELSEVIER PUBLICATIONS, CAMBRIDGE, GB, vol. 20, no. 9, 1 September 2002 (2002-09-01), pages 395-401, XP004374664, ISSN: 0167-7799, DOI: 10.1016/S0167-7799(02)02022-X *

Also Published As

Publication number Publication date
US20150057162A1 (en) 2015-02-26
WO2013136095A1 (en) 2013-09-19
GB2500243A (en) 2013-09-18
GB201204605D0 (en) 2012-05-02
GB201418188D0 (en) 2014-11-26

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